Package: rGREAT 2.15.0

Zuguang Gu

rGREAT: GREAT Analysis - Functional Enrichment on Genomic Regions

GREAT (Genomic Regions Enrichment of Annotations Tool) is a type of functional enrichment analysis directly performed on genomic regions. This package implements the GREAT algorithm (the local GREAT analysis), also it supports directly interacting with the GREAT web service (the online GREAT analysis). Both analysis can be viewed by a Shiny application. rGREAT by default supports more than 600 organisms and a large number of gene set collections, as well as self-provided gene sets and organisms from users. Additionally, it implements a general method for dealing with background regions.

Authors:Zuguang Gu [aut, cre]

rGREAT_2.15.0.tar.gz
rGREAT_2.15.0.zip(r-4.7)rGREAT_2.15.0.zip(r-4.6)rGREAT_2.15.0.zip(r-4.5)
rGREAT_2.15.0.tgz(r-4.6-x86_64)rGREAT_2.15.0.tgz(r-4.6-arm64)rGREAT_2.15.0.tgz(r-4.5-x86_64)rGREAT_2.15.0.tgz(r-4.5-arm64)
rGREAT_2.15.0.tar.gz(r-4.7-arm64)rGREAT_2.15.0.tar.gz(r-4.7-x86_64)rGREAT_2.15.0.tar.gz(r-4.6-arm64)rGREAT_2.15.0.tar.gz(r-4.6-x86_64)
rGREAT_2.15.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rGREAT/json (API)

# Install 'rGREAT' in R:

install.packages('rGREAT', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jokergoo/rgreat/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:rGREAT-2.15.0(bioc 3.24)rGREAT-2.14.0(bioc 3.23)

genesetenrichment go pathways software sequencing wholegenome genomeannotation coverage cpp

10.06 score 98 stars 1 packages 525 scripts 5 mentions 31 exports 115 dependencies

Last updated from:108d370ebb. Checks:1 ERROR, 13 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	395
linux-devel-arm64	OK	453
linux-devel-x86_64	OK	649
source / vignettes	OK	440
linux-release-arm64	OK	477
linux-release-x86_64	OK	617
macos-release-arm64	OK	381
macos-release-x86_64	OK	720
macos-oldrel-arm64	OK	545
macos-oldrel-x86_64	OK	926
windows-devel	OK	496
windows-release	OK	451
windows-oldrel	OK	488
wasm-release	OK	291

Exports:availableCategories availableOntologies extendTSS extendTSSFromDataFrame extendTSSFromOrgDb extendTSSFromTxDb getEnrichmentTable getEnrichmentTables getGapFromUCSC getGeneSetsFromBioMart getGeneSetsFromOrgDb getGenesFromGencode getGenomeDataFromNCBI getGREATDefaultTSS getKEGGGenome getKEGGPathways getRefSeqGenesFromUCSC getRegionGeneAssociations getTSS great great_opt GreatJob GreatObject plotRegionGeneAssociationGraphs plotRegionGeneAssociations plotVolcano randomRegions randomRegionsFromBioMartGenome read_gmt shinyReport submitGreatJob

Dependencies:abind AnnotationDbi askpass base64enc BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob bslib cachem cigarillo circlize cli codetools colorspace commonmark cpp11 crayon crosstalk curl DBI DelayedArray digest doParallel DT evaluate fastmap fontawesome foreach formatR fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GetoptLong GlobalOptions glue GO.db highr hms htmltools htmlwidgets httpuv httr IRanges iterators jquerylib jsonlite KEGGREST knitr lambda.r later lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl org.Hs.eg.db otel pkgconfig png prettyunits progress promises R6 rappdirs RColorBrewer Rcpp RCurl restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Arrays S4Vectors sass Seqinfo shape shiny snow sourcetools SparseArray SummarizedExperiment sys tinytex TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene UCSC.utils vctrs withr xfun XML xtable XVector yaml

The rGREAT package

Rendered fromrGREAT.Rmdusingknitr::rmarkdown

Last update: 2024-02-27
Started: 2015-02-13

Help page	Topics
Available ontology categories of the GREAT job	availableCategories availableCategories,GreatJob-method
All available ontology names of the GREAT job	availableOntologies availableOntologies,GreatJob-method
Extend TSS	extendTSS
Extend TSS	extendTSSFromDataFrame
Extend TSS	extendTSSFromOrgDb
Extend TSS	extendTSSFromTxDb
Method dispatch page for getEnrichmentTable	getEnrichmentTable
Get a single enrichment table from GREAT web server	getEnrichmentTable,GreatJob-method
Get enrichment table	getEnrichmentTable,GreatObject-method
Method dispatch page for getEnrichmentTables	getEnrichmentTables
Get enrichment tables from GREAT web server	getEnrichmentTables,GreatJob-method
Get enrichment table	getEnrichmentTables,GreatObject-method
Get gap regions from UCSC	getGapFromUCSC
Get GO gene sets from BioMart	getGeneSetsFromBioMart
Get GO gene sets from OrgDb object	getGeneSetsFromOrgDb
Get Gencode genes	getGenesFromGencode
Get genome data from NCBI	getGenomeDataFromNCBI
Get built-in TSS from GREAT	getGREATDefaultTSS
Get the corresponding assembly id for a kegg organism	getKEGGGenome
Get KEGG pathway gene sets	getKEGGPathways
Get RefSeq genes from UCSC	getRefSeqGenesFromUCSC
Method dispatch page for getRegionGeneAssociations	getRegionGeneAssociations
Get region-gene associations	getRegionGeneAssociations,GreatJob-method
Get region-gene associations	getRegionGeneAssociations,GreatObject-method
Get the internally used TSS	getTSS
Perform GREAT analysis	great
Global parameters for rGREAT	great_opt
Constructor method for GreatJob class	GreatJob
Class to store and retrieve GREAT results	GreatJob-class
Constructor method for GreatObject class	GreatObject
Class for local GREAT analysis	GreatObject-class
Plot region-gene associations	plotRegionGeneAssociationGraphs plotRegionGeneAssociationGraphs,GreatJob-method
Method dispatch page for plotRegionGeneAssociations	plotRegionGeneAssociations
Plot region-gene associations	plotRegionGeneAssociations,GreatJob-method
Plot region-gene associations	plotRegionGeneAssociations,GreatObject-method
Method dispatch page for plotVolcano	plotVolcano
Make volcano plot	plotVolcano,GreatJob-method
Make volcano plot	plotVolcano,GreatObject-method
Generate random regions	randomRegions
Generate random regions from a BioMart genome	randomRegionsFromBioMartGenome
Read gmt gene sets file	read_gmt
Reduce by start and end	reduce_by_start_and_end
Method dispatch page for shinyReport	shinyReport
Shiny app on the GreatJob object	shinyReport,GreatJob-method
Shiny app on the GreatObject object	shinyReport,GreatObject-method
Perform online GREAT analysis	submitGreatJob

Package: rGREAT 2.15.0

rGREAT: GREAT Analysis - Functional Enrichment on Genomic Regions

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Usage by other packages (reverse dependencies)